Zeiss CZI

Benjamin Gilbert bgilbert at cs.cmu.edu
Tue Nov 18 01:38:18 EST 2014

On 11/16/2014 03:44 AM, Mario Emmenlauer wrote:
> I've seen an email conversation from summer where support for Zeiss
> CZI was mentioned - is there (preliminary) support for this format?
> Can I help with some testing or something?

Hi Mario,

Yaël Balbastre and Nicolas Souedet were working on adding CZI support:


As I understand it, their changes are not yet complete, and I haven't 
heard from them in a while.

For now, the best way to help is by contributing sample slides.  We do 
have some CZI files provided by the community, but what we really need 
now is for someone to spend a couple hours with a scanner and collect a 
set of scans in a rigorous way.  Ideally, we'd like samples of every 
major feature supported by the format, including:

- A couple JPEG slides
- A couple JPEG XR slides
- An LZW slide, if supported (I am unclear on that)
- A slide with multiple regions of interest, if supported
- Fluorescence scans
- Time-lapse, Z-stacks, etc.

It's best if the scans are of real specimens (instead of a blank slide) 
but the specimens can be anything that is convenient.

For the scans to be the most useful, we also need a signed permission 
letter allowing us to distribute these samples in the openslide-testdata 
dataset.  This allows us to use the samples in automated test cases, and 
allows others to use them for their own testing.  I can provide the 
wording for this letter upon request.

--Benjamin Gilbert

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